6LI0

Crystal structure of GPR52 in complex with agonist c17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis of ligand recognition and self-activation of orphan GPR52.

Lin, X.Li, M.Wang, N.Wu, Y.Luo, Z.Guo, S.Han, G.W.Li, S.Yue, Y.Wei, X.Xie, X.Chen, Y.Zhao, S.Wu, J.Lei, M.Xu, F.

(2020) Nature 579: 152-157

  • DOI: 10.1038/s41586-020-2019-0
  • Primary Citation of Related Structures:  
    6LI0, 6LI1, 6LI2, 6LI3

  • PubMed Abstract: 
  • GPR52 is a class-A orphan G-protein-coupled receptor that is highly expressed in the brain and represents a promising therapeutic target for the treatment of Huntington's disease and several psychiatric disorders 1,2 . Pathological malfunction of GPR52 signalling occurs primarily through the heterotrimeric G s protein 2 , but it is unclear how GPR52 and G s couple for signal transduction and whether a native ligand or other activating input is required ...

    GPR52 is a class-A orphan G-protein-coupled receptor that is highly expressed in the brain and represents a promising therapeutic target for the treatment of Huntington's disease and several psychiatric disorders 1,2 . Pathological malfunction of GPR52 signalling occurs primarily through the heterotrimeric G s protein 2 , but it is unclear how GPR52 and G s couple for signal transduction and whether a native ligand or other activating input is required. Here we present the high-resolution structures of human GPR52 in three states: a ligand-free state, a G s -coupled self-activation state and a potential allosteric ligand-bound state. Together, our structures reveal that extracellular loop 2 occupies the orthosteric binding pocket and operates as a built-in agonist, conferring an intrinsically high level of basal activity to GPR52 3 . A fully active state is achieved when G s is coupled to GPR52 in the absence of an external agonist. The receptor also features a side pocket for ligand binding. These insights into the structure and function of GPR52 could improve our understanding of other self-activated GPCRs, enable the identification of endogenous and tool ligands, and guide drug discovery efforts that target GPR52.


    Organizational Affiliation

    Centre for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China. xufei@shanghaitech.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chimera of G-protein coupled receptor 52 and FlavodoxinA468Homo sapiensDesulfovibrio vulgaris str. HildenboroughMutation(s): 8 
Gene Names: GPR52DVU_2680
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2T5 (Homo sapiens)
Explore Q9Y2T5 
Go to UniProtKB:  Q9Y2T5
PHAROS:  Q9Y2T5
Find proteins for P00323 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P00323 
Go to UniProtKB:  P00323
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EN6 (Subject of Investigation/LOI)
Query on EN6

Download Ideal Coordinates CCD File 
B [auth A]N-(2-hydroxyethyl)-5-(hydroxymethyl)-3-methyl-1-[2-[[3-(trifluoromethyl)phenyl]methyl]-1-benzothiophen-7-yl]pyrazole-4-carboxamide
C24 H22 F3 N3 O3 S
VJMRKWPMFQGIPI-UHFFFAOYSA-N
 Ligand Interaction
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
OLC (Subject of Investigation/LOI)
Query on OLC

Download Ideal Coordinates CCD File 
D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , L [auth A] , 
D [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  L [auth A],  M [auth A],  N [auth A],  P [auth A],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  U [auth A],  V [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
FLC
Query on FLC

Download Ideal Coordinates CCD File 
O [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth A], BA [auth A], CA [auth A], K [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EN6 BindingDB:  6LI0 EC50: 21 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.97α = 90
b = 88.36β = 90
c = 156.28γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2020-03-18
    Changes: Database references